The proposed Cold Spring Harbor Laboratory Course on Proteomics is to be held July 7 - 22, 2012 and similar dates in 2013, 2014, 2015, and 2016. Proteomics is one of the pillar technologies of systems biology by which hundreds or thousands of proteins can be monitored and characterized simultaneously. In combination with genomics and metabolomics approaches, proteomics is an enabling core technology to probe biological activities in parallel, providing unprecedented analytical power into diverse biological processes in mammalian development and disease. Models of many human diseases have been developed in a wide variety of animal systems, in particular vertebrate models such as mouse, zebrafish, rat and frog, and invertebrate models such as worms and flies; and increasingly the use of new stem cell technologies is being harnessed to produce powerful in vitro models to be deployed alongside animal models. There is a growing need for implementation of systems biology approaches to these models, which necessitates an in-depth understanding of the challenges and pitfalls of various high-throughput technologies, achieved in part by hands-on and highly focused training. This intensive laboratory and lecture course will focus on cutting-edge proteomics approaches and technologies. Students will gain practical experience purifying and identifying protein complexes and posttranslational modifications using the latest technologies. In the protein profiling portion of the course, students will gain hands-on experience in several quantitative proteome analysis methods, including two-dimensional gel electrophoresis and isotopic labeling strategies. Students will be trained to use DIGE, or differential in-gel electrophoresis, for gel-based protein quantification. Differentially expressed proteins will be statistically determined using advanced gel analysis software, and identified using MALDI mass spectrometry. For shotgun proteomics analysis, students will be taught label-free and covalent isotopic-labeling approaches to differentially profile changes in proteomes. Students will be trained in high-sensitivity microcapillary liquid chromatography coupled with nanospray-ESI and tandem mass spectrometry. Both single dimension and multidimensional separation methods coupled to mass spectrometry will be taught. In the targeted proteomics section of the course, students will be taught to analyze and process shotgun proteomics data to develop SRM/MRM assays to accurately identify and quantify selected proteins. Students will be trained to select and design transitions for targeted peptides and to setup and perform SRM/MRM mass spectrometry assays. They will learn to process and interpret the acquired data to measure and validate changing quantities of targeted proteins in a variety of biological samples. For all sections of the course, a strong emphasis will be placed on data analysis. Outside lecturers will discuss proteomics topics and methods not directly covered in the course including protein arrays, imaging by mass spectrometry, de novo sequence analysis, top-down proteomics, advanced mass spectrometry methods, and functional proteomics. The overall aim of the course is to provide each student with the fundamental knowledge and hands-on experience necessary to be able to perform and analyze proteomics experiments. The long term goal is to train students to identify new opportunities and applications for proteomics approaches in their biological research and to learn how to integrate these into systems biology and model organism approaches to human biology and health.